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qc-basic.workflow.cwl
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qc-basic.workflow.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
jobid: string
sequences: File
kmerLength:
type: int[]?
default: [6]
outputs:
seqStatFile:
type: File
outputSource: formatSequenceStats/stats
seqBinFile:
type: File
outputSource: formatSequenceStats/bins
qcStatFile:
type: File
outputSource: formatQcStats/stats
qcSummaryFile:
type: File
outputSource: formatQcStats/summary
steps:
sequenceStats:
run: ../Tools/seq_length_stats.tool.cwl
in:
sequences: sequences
outName:
source: jobid
valueFrom: $(self).075.seq.stats
lenBin:
source: jobid
valueFrom: $(self).075.length.bin
gcBin:
source: jobid
valueFrom: $(self).075.gc.bin
out: [statOut, lenBinOut, gcBinOut]
drisee:
run: ../Tools/drisee.tool.cwl
in:
sequences: sequences
out: [info, stats]
kmer:
run: ../Tools/kmer-tool.tool.cwl
scatter: "#kmer/length"
scatterMethod: dotproduct
in:
sequences: sequences
length: kmerLength
format:
valueFrom: histo
prefix:
source: jobid
valueFrom: $(self).075
out: [stats]
consensus:
run: ../Tools/consensus.tool.cwl
in:
sequences: sequences
stats: sequenceStats/statOut
output:
source: jobid
valueFrom: $(self).075.consensus.stats
out: [summary, consensus]
formatSequenceStats:
run: ../Tools/format_seq_stats.tool.cwl
in:
output_prefix:
source: jobid
valueFrom: $(self).075.qc
sequence_stats: sequenceStats/statOut
sequence_lengths: sequenceStats/lenBinOut
sequence_gc: sequenceStats/gcBinOut
out: [stats, bins]
formatQcStats:
run: ../Tools/format_qc_stats.tool.cwl
in:
outPrefix:
source: jobid
valueFrom: $(self).075.qc
driseeStat: drisee/stats
driseeInfo: drisee/info
consensus: consensus/consensus
kmer: kmer/stats
out: [stats, summary]